RESUMEN
The prickly blue poppy (Meconopsis horridula Hook. f. & Thomson) is a traditional Tibetan medicinal herb with high values. In this study, its chloroplast genome was determined to be 153,761 bp in length with an A + T-biased base composition, and comprises a pair of inverted repeat (IR) regions (26,030 bp), separated by a large single-copy (LSC) region (83,803 bp) and a small single-copy (SSC) region (17,898 bp). A total of 113 gene species were annotated, with 20 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis suggests that M. horridula is closely related to Meconopsis racemosa Maxim.
RESUMEN
Cyperus fuscus known as brown flatsedge plays an important role in sand fixation and water purification. The first complete chloroplast genome sequences of pioneering plant C. fuscus were reported in this study. The complete chloroplast genome was 167,660 bp in length, containing a large single copy region (LSC) of 79,790 bp and a small single copy region (SSC) of 12,192 bp, which were separated by a pair of 37,839 bp inverted repeat regions (IRs). The chloroplast genome contains 135 genes, including 92 protein-coding genes, eight ribosomal RNA genes, and 35 transfer RNA genes. The overall GC content is 36.3%, while the corresponding values of the LSC, SSC, and IR region are 35.1%, 28.3%, and 38.5%, respectively. Further, the maximum-likelihood phylogenetic analysis showed a strong sister relationship with Cyperus difformis in Cyperaceae. Our findings provide a foundation for further study of chloroplast genome evolution and genetics information in C. fuscus.
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Chloroplast (cp) genome sequences have become a useful popular tool for population and phylogeny recently. It is little known about genetics information of Lavandula angustifolia. Here, the complete chloroplast genome of the L. angustifolia has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 153,448 bp in size, and comprises of a pair of inverted repeat (IR) regions of 25,632 bp each, a large single-copy (LSC) region of 84,588 bp and a small single-copy (SSC) region of 17,596 bp. The total GC content is 38.0%, while the corresponding values of the LSC, SSC, and IR regions are 36.2, 31.8, and 43.2%, respectively. The chloroplast genome contains 132 genes, including 88 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The Maximum-Likelihood phylogenetic analysis showed a strong sister relationship with Salvia miltiorrhiza in Lamiaceae. These findings provide a foundation for further investigation of cp genome evolution in L. angustifolia and other higher plants.
RESUMEN
Chloroplast (cp) genome sequences have become a useful tool for phylogeneitc and evolutionary study in recent reports. Here the complete chloroplast genome of the Paphiopedilum tranlimianum has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 162,127 bp in size, and comprises of a pair of inverted repeat (IR) regions of 31,457 bp each, a large single-copy (LSC) region of 91,711 bp, and a small single-copy (SSC) region of 7,502 bp. The total GC content is 35.4%, while the corresponding values of the LSC, SSC, and IR regions are 32.7%, 26.9%, and 40.9%, respectively. The chloroplast genome contains 133 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. Three genes (ndhA, ndhE, and ndhI) are pseudogenized or lost in its cpDNA. The Maximum-Likelihood phylogenetic analysis showed a close relationship with P. niveum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.
RESUMEN
Chloroplast (cp) genome sequences became a widely used tool for evolutionary and phylogenetic studies in plants. Abies chensiensis (Pinaceae: Abietoideae) is an endangered species endemic to China. To understand its evolutionary characteristics, the complete chloroplast genome of the A. chensiensis has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 121,784 bp in length and without a typical quadripartite structure due to the loss of IR region. The total GC content of whole genome sequence is 38.3%. The chloroplast genome encodes 109 genes, including 75 protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes. Among them, 35 genes involved in photosynthesis, while 58 genes involved in self-replication. The Maximum-Likelihood phylogenetic analysis showed a strong sister relationship with A. nephrolepis and A. koreana in Abietoideae. Our findings provide fundamental information for further evolutionary and phylogenetic researches of Abietoideae.
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Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis, which becomes a popular tool for population and phylogeny in a recent report. Here, the complete chloroplast genome of the Paphiopedilum wardii has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 169,820 bp in size and comprises a pair of inverted repeat (IR) regions of 33,641 bp each, a large single-copy (LSC) region of 98,872 bp and a small single-copy (SSC) region of 3666 bp. The total GC content is 33.8%, while the corresponding values of the IR regions, LSC, and SSC and are 38.7%, 31.7% and 26.7%, respectively. The chloroplast genome contains 151 genes, including 91 protein-coding genes, eight ribosomal RNA genes and 52 transfer RNA genes. Two genes (ndhA and ndhB) are pseudogenized or lost in its cpDNA. The maximum-likelihood phylogenetic analysis showed a close relationship with P. armeniacum in Orchidaceae. Our findings provide useful information for phylogenetic and evolutionary research of Paphiopedilum species.
RESUMEN
Chloroplast (cp) genome sequences provide a valuable source for phylogenetic analysis. It becomes a popular useful tool for population and phylogeny in recently report. Here, the complete chloroplast genome of the Isatis indigotica has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 156,670 bp in size and comprises a pair of inverted repeat (IR) regions of 26,995 bp each, a large single-copy (LSC) region of 84,907 bp and a small single-copy (SSC) region of 17,773 bp. The total GC content is 36.5%, while the corresponding values of the LSC, SSC and IR region are 34.2%, 29.7% and 42.3%, respectively. The chloroplast genome contains 140 genes, including 94 protein-coding genes. The phylogenetic analysis showed a strong sister relationship with Raphanus sativus in Brassicaceae. These findings provide a foundation for further investigation of cp genome evolution in I. indigotica and other higher plants.
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Here we report the first full mitochondrial genome sequence for a white shark caught in the Atlantic Ocean. The mitochondrial genome is 16,745 bp in length and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region. The base composition of this mtDNA lineage is A: 30.7%, C: 26.9%, G: 13.8%, and T: 28.6%. In concordance with previous population genetic studies, the Atlantic caught individual forms a separate lineage from individuals caught on either side of the Pacific Ocean.
RESUMEN
Dioscorea zingiberensis (Dioscoreceae) is an important medicinal plant endemic to China. Here, its chloroplast genome sequence is reconstructed from the whole-genome Illumina sequencing data. The circular genome is 153,970 bp in length, and comprises a pair of inverted repeat (IR) regions of 25,491 bp each, a large single-copy (LSC) region of 83,950 bp and a small single-copy (SSC) region of 19,038 bp. The chloroplast genome contains 132 genes, including 86 protein-coding genes (79 PCG species), 8 ribosomal RNA genes (four rRNA species) and 38 transfer RNA genes (30 tRNA species). Out of these genes, 10 harbor a single intron, and 7 contain a couple of introns. The overall A + T content of the whole genome is 62.8%, while the corresponding values of the LSC, SSC and IR regions are 64.9%, 68.8% and 57.0%, respectively.
Asunto(s)
Dioscorea/genética , Genoma del Cloroplasto/genética , ADN de Cloroplastos/genética , Dioscorea/clasificación , Orden Génico/genética , Genoma de Planta/genética , Intrones/genética , Filogenia , ARN de Transferencia/genética , Análisis de Secuencia de ADNRESUMEN
The complete chloroplast genome of the mulberry Morus notabilis (Moreae) has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 158,680 bp in size, and comprises a pair of inverted repeat (IR) regions of 25,717 bp each, a large single-copy (LSC) region of 87,470 bp and a small single-copy (SSC) region of 19,776 bp. The total A+T content is 63.6%, while the corresponding values of the LSC, SSC and IR region are 65.9%, 70.7% and 57.1%, respectively. The chloroplast genome contains 129 genes, including 84 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes and 37 transfer RNA (tRNA) genes. The maximum likelihood (ML) phylogenetic analysis revealed that M. notabilis was more related to its congeners than to the others.
Asunto(s)
Genoma del Cloroplasto/genética , Morus/genética , ADN de Cloroplastos/genética , Genoma de Planta/genética , Morus/clasificación , Filogenia , ARN Ribosómico/genética , ARN de Transferencia/genética , Análisis de Secuencia de ADNRESUMEN
Complete chloroplast genome sequence is very useful for studying the phylogenetic and evolution of species. In this study, the complete chloroplast genome of Dendrobium strongylanthum was constructed from whole-genome Illumina sequencing data. The chloroplast genome is 153 058 bp in length with 37.6% GC content and consists of two inverted repeats (IRs) of 26 316 bp. The IR regions are separated by large single-copy region (LSC, 85 836 bp) and small single-copy (SSC, 14 590 bp) region. A total of 130 chloroplast genes were successfully annotated, including 84 protein coding genes, 38 tRNA genes, and eight rRNA genes. Phylogenetic analyses showed that the chloroplast genome of Dendrobium strongylanthum is related to that of the Dendrobium officinal.
Asunto(s)
Dendrobium/clasificación , Dendrobium/genética , Genoma del Cloroplasto , Genómica , Genes del Cloroplasto , Genómica/métodos , Filogenia , Análisis de Secuencia de ADN , Secuenciación Completa del GenomaRESUMEN
The complete chloroplast genome of the medicinal plant Rheum palmatum L. (Polygonaceae) has been reconstructed from the whole-genome Illumina sequencing data. The genome is 161 541 bp in length, and exhibits a typical quadripartite structure of the large (LSC, 86 518 bp) and small (SSC, 13 111 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 30 956 bp each). The chloroplast genome contains 131 genes, including 84 protein-coding genes (78 PCG species), eight ribosomal RNA genes (four rRNA species) and 37 transfer RNA genes (28 tRNA species). Phylogenetic tree based on the maximum parsimony (MP) analysis of 65 chloroplast protein-coding genes for 13 taxa demonstrated a close relationship between R. palmatum and Fagopyrum esculentum subsp. ancestrale in Polygonaceae.
Asunto(s)
Genoma del Cloroplasto , Rheum/clasificación , Rheum/genética , Composición de Base , Genes del Cloroplasto , Genes de Plantas , Tamaño del Genoma , Sistemas de Lectura Abierta , Filogenia , Plantas Medicinales/clasificación , Plantas Medicinales/genética , Análisis de Secuencia de ADN , Secuenciación Completa del GenomaRESUMEN
The complete mitochondrial genome of the common buckeye Junonia coenia (Insecta: Lepidoptera: Nymphalidae) was reconstructed from whole-genome Illumina sequencing data with an average coverage of 1213×. The circular genome is 15 222 bp in length, and consists of 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs are initiated with ATN codons. Five PCGs (COX1, COX2, CYTB, ND2 & ND4) harbor an incomplete termination codon T--, while all the others are terminated with TAA. The nucleotide composition is highly asymmetric (39.6% A, 11.6% C, 7.7% G & 41.1% T) with an overall GC content of 19.3%. Phylogenetic analysis suggested that J. coenia is phylogenetically closer to its congeners and its consubfamilial counterparts than to the other taxa.
Asunto(s)
ADN Mitocondrial/genética , Genoma Mitocondrial/genética , Lepidópteros/genética , Animales , Composición de Base/genética , Secuencia de Bases/genética , Evolución Biológica , Mariposas Diurnas/genética , Orden Génico , Genes Mitocondriales/genética , Genoma/genética , Insectos/genética , Mitocondrias/genética , Filogenia , Análisis de Secuencia de ADN/métodosRESUMEN
The complete mitochondrial genome of the navel orangeworm Amyelois transitella (Insecta: Lepidoptera: Pyralidae) was assembled from Illumina sequencing reads (Illumina Inc., San Diego, CA). The genome is a double-stranded circular molecule of 15 205 bp, comprising 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region. All PCGs are initiated with ATN codons, except for COX1 with the putative CGA initiation codon. Six PCGs (COX1, COX2, CYTB, ND2, ND3, and ND4) harbor an incomplete termination codon T, while all the others are terminated with TAA (ATP6, ATP8, COX3, ND1, ND4, and ND6) or TAG (ND4L). The base composition is highly biased (37.9% A, 12.6% C, 7.8% G, and 41.7% T) with an overall A + T content of 79.6%. Phylogenetic analysis indicated that A. transitella is more phylogenetically related to its confamilial counterparts than to those from the family Crabidae.
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Genoma Mitocondrial , Lepidópteros/genética , Animales , Composición de Base , Codón Iniciador , Codón de Terminación , ADN Mitocondrial/química , ADN Mitocondrial/aislamiento & purificación , ADN Mitocondrial/metabolismo , Complejo IV de Transporte de Electrones/química , Complejo IV de Transporte de Electrones/genética , Complejo IV de Transporte de Electrones/metabolismo , Proteínas de Insectos/química , Proteínas de Insectos/genética , Proteínas de Insectos/metabolismo , Lepidópteros/clasificación , NADH Deshidrogenasa/química , NADH Deshidrogenasa/genética , NADH Deshidrogenasa/metabolismo , Sistemas de Lectura Abierta/genética , Filogenia , ARN Ribosómico/química , ARN Ribosómico/genética , ARN de Transferencia/química , ARN de Transferencia/genética , Análisis de Secuencia de ADNRESUMEN
The complete mitochondrial genome of the Scarlet Tiger moth Callimorpha dominula (Insecta: Lepidoptera: Arctiidae) has been reconstructed from the whole-genome Illumina sequencing data. This circular genome is 15 496 bp in size, and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one A + T-rich D-loop or control region. Most PCGs are initiated with the ATN codons, except for COX1 with the unusual CGA as its initiation codon. Four PCGs (COX1, COX2, ND3, and ND4) are terminated with incomplete codon T, ND4L uses TAG as its termination codon, while all the other eight PCGs employ the usual ATN codons. The nucleotide composition is highly asymmetric (40.1% A, 40.9% T, 7.6% G, and 11.4% C) with an overall A + T content of 81.0%. The phylogenetic analysis based on the neighbor-joining (NJ) method suggests that C. dominula is more phylogenetically related to its confamilial counterparts than to those from other families.
Asunto(s)
Genoma Mitocondrial , Mariposas Nocturnas/genética , Animales , ADN Mitocondrial/genética , Proteínas de Insectos/genética , Proteínas Mitocondriales/genética , Filogenia , Secuenciación Completa del GenomaRESUMEN
The complete mitochondrial genome of the Tiger Longwing Heliconius hecale has been reconstructed from whole-genome Illumina sequencing data with an average coverage of 1507×. The circular genome is 15,338 bp in length, consisting of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop or control region. All PCGs initiated with ATN codons, except for the COI and ND1 genes with CGA and TTG as their start codons, respectively. Three PCGs (COI, COII and ND4) have an incomplete stop codon T, the ND3 gene harbors the stop codon TAG, while all the other PCGs terminated with the TAA codon. The nucleotide composition is highly asymmetric (39.5% A, 42.1% T, 7.5% G, and 10.9% C) with an overall GC content of 18.4%.
Asunto(s)
Mariposas Diurnas/genética , Genoma Mitocondrial , Análisis de Secuencia de ADN/métodos , Animales , Composición de Base , Tamaño del Genoma , Mitocondrias/genéticaRESUMEN
The complete mitogenome of the Cydno Longwing Heliconius cydno has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 15,367 bp in length, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. PCGs are mostly initiated with the ATN codons (COII, COIII, Cytb, ND2, ND3, ND4, ND4L, ND5, ND6, ATP6 & ATP8), except for the ND1 and COI genes with TTG and the unusual CGA as their initiation codons, respectively. Some PCGs harbor TAG (ND3) or incomplete termination codon T (COI, COII & ND4), while all the others use TAA as their termination codons. The nucleotide composition is highly asymmetric (39.3% A, 42.1% T, 7.6% G, 11.0% C) with an overall GC content of 18.6%.
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Mariposas Diurnas/genética , Genoma Mitocondrial , Mitocondrias/genética , Animales , Composición de Base , Tamaño del Genoma , Genoma de los Insectos , Análisis de Secuencia de ADN/métodosRESUMEN
The complete mitogenome of the geophilous grasshopper Trilophidia annulata was reconstructed from whole-genome Illumina sequencing data. After annotation, the circular genome was obtained with 16,501 bp in length, and typically consisted of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. All PCGs were initiated with ATN codons, except ND2 with the start codon GTG. Most of the PCGs used TAA as their stop codons, while the others used TAG as stop codons (COX1, COX3&ND1). The nucleotide composition was asymmetric (42.3% A, 15.0% C, 11.0% G, 31.8% T) with an overall GC content of 25.9%. These data would contribute to the design of novel molecular markers for population and evolutionary research of T. annulata.
Asunto(s)
Genoma Mitocondrial , Saltamontes/genética , Animales , Composición de Base , Codón Iniciador/genética , Codón de Terminación/genética , Saltamontes/clasificación , Proteínas de Insectos/genética , Filogenia , ARN Ribosómico/genética , ARN de Transferencia/genéticaRESUMEN
The complete mitochondrial genome of Formica selysi has been assembled from Illumina sequencing data with an average coverage of 2733X. The circular genome was 16,752 bp in length, and consists of 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs) and one D-loop region. All PCGs initiated with ATN codons and terminated with the TAA codon. The nucleotide composition was highly asymmetric (40.33% A, 11.07% C, 5.66% G and 42.94% T) with an overall GC content of 16.73%. Unlike those of most other insects, the mitochondrial genome of F. selysi was characterized by an obviously high proportion of intergenic spacers. These data would contribute to the evolutionary studies of this and related ant taxa.
Asunto(s)
Hormigas/genética , Genoma Mitocondrial , Animales , Composición de Base , Codón/genética , ADN Intergénico/química , ADN Intergénico/genética , Proteínas de Insectos/genética , ARN Ribosómico/genética , ARN de Transferencia/genéticaRESUMEN
The complete mitochondrial genome of the Sara Longwing Heliconius sara has been reconstructed from the whole-genome Illumina sequencing data. The mitochondrial genome is 15,372 bp in size with the highly asymmetric overall A + T content of 80.6%. Annotation of mitochondrial genome revealed a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs) and 1 D-loop region. Most PCGs are initiated with the ATN codons, while COX1 and ND1 start with CGA and TTG, respectively. COX1, COX2, and ND4 harbor the incomplete stop codon T, while all the others are terminated with the TAR codons. The complete mitochondrial genome of H. Sara would contribute to our further understanding of the phylogeny and evolution of the genus Heliconius and related taxa.